A fuel cell system that is capable of suppressing temperature change of the fuel cell under a low temperature environment after the operation has stopped, suppressing freezing due to condensation, and ensuring a preferable start thereafter. The fuel cell system comprises: a fuel cell that generates electric power through an electrochemical reaction between air and a hydrogen gas; a gas supply section that supplies air and the hydrogen gas to an air supply path, a fuel supply path and a hydrogen circulation path which are connected to the fuel cell by a compressor and a hydrogen pump; a cooling section that cools the fuel cell by making a cooling path connected to the fuel cell to circulate by a pump the cooling water that is cooled by a radiator; and a control section.